Jasmine Y. Young
Research Professor, Rutgers, The State University of New Jersey
Biocuration Team Lead, RCSB Protein Data Bank
Global Project Lead, worldwide Protein Data Bank
Center for Integrative Proteomics Research

Tel: 848-445-4920
Email Address: jasmine.young@rcsb.org
jasmin@rcsb.rutgers.edu
  Education
Highest Earned Degree
Ph.D., University of Florida, Chemistry, 1996
Certificates and Licenses Held
Leadership Development Certificate, Center for management development at Rutgers, 2009
  Research Interests
Description of Research and Scholarly or Creative Objectives
Since 2008, in my role as RCSB PDB Biocuration Team Lead, I oversee practices, management, and OneDep tool developments for data deposition, curation, validation, and remediation of the PDB archive to ensure data standardization, high quality and uniformity. Collaborating with wwPDB partners globally, I represent RCSB PDB to set common annotation practices and procedures, to establish daily operation and weekly release procedures, and to set data standards at the PDB.

As a Global Project Lead since 2015, I manage international wwPDB projects including OneDep tool and data remediation across wwPDB partner sites. I lead our on-going data analysis and strategic planning for improved PDB data representation and OneDep system. Most recently, these remediation efforts have enabled data standardization to V5.0 PDBx/mmCIF dictionary. The OneDep system has been improved since the initial deployment and has already been used for the deposition and annotation of all new PDB entries.
  Publications
Articles in Refereed Journals
Goodsell DS, Zardecki C, Di Costanzo L, Duarte JM, Hudson BP, Persikova I, Segura J, Shao C, Voigt M, Westbrook JD, Young JY, Burley SK. RCSB Protein Data Bank: Enabling biomedical research and drug discovery. Protein Sci. 2020 Jan;29(1):52-65. doi: 10.1002/pro.3730. Epub 2019 Nov 29. PubMed PMID: 31531901; PubMed Central PMCID: PMC6933845.
Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):451-454. doi: 10.1107/S2059798319004522. PMID: 3098826.
Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Di Costanzo L, Christie C, Dalenberg K, Duarte JM, Dutta S, Feng Z, Ghosh S, Goodsell DS, Green RK, Guranovic V, Guzenko D, Hudson BP, Kalro T, Liang Y, Lowe R, Namkoong H, Peisach E, Periskova I, Prlic A, Randle C, Rose A, Rose P, Sala R, Sekharan M, Shao C, Tan L, Tao YP, Valasatava Y, Voigt M, Westbrook J, Woo J, Yang H, Young J, Zhuravleva M, Zardecki C. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. 2019 Jan 8;47(D1):D464-D474. doi: 10.1093/nar/gky1004. PMID: 30357411.
wwPDB consortium. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 2019 Jan 8;47(D1):D520-D528. doi: 10.1093/nar/gky949. PMID: 30357364

Burley SK, Berman HM, Christi, C, Duarte, JM, Feng Z, Westbrook J, Young J, Zardecki C. RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. Protein Sci. 2018 Jan;27(1):316-330. doi: 10.1002/pro.3331. PMID: 29067736.
Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP1, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay002. PMID: 29688351
Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K , Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, and Kleywegt GJ. Validation of the Structures in the Protein Data Bank. 2017 Dec 5;25(12):1916-1927. doi: 10.1016/j.str.2017.10.009. PMID: 29174494
Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PM, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. Structure. 2017 Mar 7;25(3):536-545. doi: 10.1016/j.str.2017.01.004. Epub 2017 Feb 9. PubMed PMID: 28190782; PubMed Central PMCID: PMC5360273.
Shao C, Yang H, Westbrook JD, Young JY, Zardecki C, Burley SK. Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive. Structure. 2017 Mar 7;25(3):458-468. doi: 10.1016/j.str.2017.01.013. Epub 2017 Feb 16. PubMed PMID: 28216043.
Rose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK. The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 2017 Jan 4;45(D1):D271-D281. doi: 10.1093/nar/gkw1000. Epub 2016 Oct 27. PubMed PMID: 27794042; PubMed Central PMCID: PMC5210513.
Yang H, Peisach E, Westbrook JD, Young J, Berman HM, Burley SK. DCC: a Swiss army knife for structure factor analysis and validation. J Appl Crystallogr. 2016 Apr 18;49(Pt 3):1081-1084. eCollection 2016 Jun 1. PubMed PMID: 27275151; PubMed Central PMCID: PMC4886994.
Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure. 2016 Apr 5;24(4):502-508. doi: 10.1016/j.str.2016.02.017. PubMed PMID: 27050687; PubMed Central PMCID: PMC5070601.
 Westbrook JD, Shao C, Feng Z, Zhuravleva M, Velankar S, Young J. The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. Bioinformatics. 2015 Apr 15;31(8):1274-8. doi: 10.1093/bioinformatics/btu789. Epub 2014 Dec 2. PubMed PMID: 25540181; PubMed Central PMCID: PMC4393513.
Rose PW, Prlić A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley SK. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 2015 Jan;43(Database issue):D345-56. doi: 10.1093/nar/gku1214. Epub 2014 Nov 26. PubMed PMID: 25428375; PubMed Central PMCID: PMC4383988.
Shuchismita Dutta, Dimitris Dimitropoulos, Zukang Feng, Irina Periskova, Sanchayita Sen, Chenghua Shao, John Westbrook, Jasmine Young, Marina Zhuravleva, Gerard Kleywegt, Helen Berman. "Improving the Representation of Peptide-Like Inhibitor and Antibiotic Molecules in the Protein Data Bank". Biopolymers. 2014 Jun;101(6):659-68. doi: 10.1002/bip.22434. PubMed PMID: 24173824; PubMed Central PMCID: PMC3992913.
Helen Berman, Buvaneswari Coimbatore Narayanan, Luigi Di Costanzo, Shuchismita Dutta, Sutapa Ghosh, Brian Hudson, Catherine L Lawson, Ezra Peisach, Andreas Prlić, Peter W Rose, Chenghua Shao, Huanwang Yang, Jasmine Young, Christine Zardecki “Trendspotting in the Protein Data Bank”. FEBS Lett., (2013) 587(8):1036-45. doi: 10.1016/j.febslet.2012.12.029
Jasmine Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John Westbrook, Marina Zhuravleva, Chenghua Shao, Ezra Peisach, Martha Quesada, Helen Berman "Chemical Annotation of Small and Peptide-Like Molecules at the Protein Data Bank". (2013) Database, doi: 10.1093/database/bat079
Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. “Outcome of the First Electron Microscopy Validation Task Force Meeting.” (2012) Structure, 20(2):205-214, doi:10.1016/j.str.2011.12.014
Peter W. Rose, Chunxiao Bi, Wolfgang F. Bluhm, Cole H. Christie, Dimitris Dimitropoulos, Shuchismita Dutta, Rachel K. Green, David S. Goodsel, Andreas Prlic´, Martha Quesada, Gregory B. Quinn, Alexander G. Ramos, John D. Westbrook, Jasmine Young, Christine Zardecki, Helen M. Berman and Philip E. Bourne. “The RCSB Protein Data Bank: new resources for research and education” (2012) Nucleic Acids Research, 1–8, doi:10.1093/nar/gks1200
Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A Blake, Michael J Cherry, Peter D'Eustachio, Robert Finn, Michelle Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica Munoz-Torres, Darren Natale, Claire O'Donovan, Francis Ouellette, Kim D Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul Schofield, Granger Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy Wu, Jasmine Young, Raja Mazumder. “Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.” (2012) Database, The Journal of Biological Databases and Curation. DOI:10.1093/database/bas036
Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE. “The RCSB Protein Data Bank: redesigned web site and web services” (2011) Nucleic Acids Res. 39: D392-D401 doi:10.1093/nar/gkq1021
Bluhm WF, Beran B, Bi C, Dimitropoulos D, Prlic A, Quinn GB, Rose PW, Shah C, Young J, Yukich B, Berman HM, Bourne PE. “Quality assurance for the query and distribution systems of the RCSB Protein Data Bank” (2011) Database doi:10.1093/database/bar003
P.E. Bourne, B. Beran, C. Bi, W.F. Bluhm, D. Dimitropoulos, Z. Feng, D.S. Goodsell, A. Prlic, G.B. Quinn, P.W. Rose, J. Westbrook, B. Yukich, J. Young, C. Zardecki, H.M. Berman. “The evolution of the RCSB Protein Data Bank website” (2011) WIREs Computational Molecular Science 1: 782-789 doi:10.1002/wcms.57
A. Kryshtafovych, J. Moult, S.G. Bartual, J.F. Bazan, H. Berman, D.E. Casteel, E. Christodoulou, J.K. Everett, J. Hausmann, T. Heidebrecht, T. Hills, R. Hui, J.F. Hunt, J. Seetharaman, A. Joachimiak, M.A. Kennedy, C. Kim, A. Linge, K. Michalska, G.T. Montelione, J.M. Otero, A. Perrakis, J.C. Pizarro, M.J. van Raaij, T.A. Ramelot, F. Rousseau, L. Tong, A.K. Wernimont, J. Young, T. Schwede “Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction” (2011) Proteins: Structure, Function, and Bioinformatics 79: 6-20 doi:10.1002/prot.23196
Dutta S, Burkhardt K, Young J, Swaminathan GJ, Matsuura T, Henrick K, Nakamura H, Berman HM. Data Deposition and Annotation at the Worldwide Protein Data Bank Mol Biotechnol” (2009) 42:1-13. doi: 10.1007/s12033-008-9127-7
K. Henrick, Z. Feng, W.F. Bluhm, D. Dimitropoulos, J.F. Doreleijers, S. Dutta, J.L. Flippen-Anderson, J. Ionides, C. Kamada, E. Krissinel, C.L. Lawson, J.L. Markley, H. Nakamura, R. Newman, Y. Shimizu, J. Swaminathan, S. Velankar, J. Ory, E.L. Ulrich, W. Vranken, J. Westbrook, R. Yamashita, H. Yang, J. Young, M. Yousufuddin and H.M. Berman.
Remediation of the Protein Data Bank archive (2008) Nucleic Acids Research 36: D426-433. doi: 10.1093/nar/gkm937
Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM. "A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing." Proteins. (2007) Proteins 69(3): 449-65. doi: 10.1002/prot.21507
Y.J. Yang, R.L. Pizzolatto, and M.C. Messmer " Internal-External Reflection Sum-Frequency Generation Spectroscopy at an Interface" J. Opt. Soc., B, 2000, 17, pp.638-645.
R.L. Pizzolatto, Y.J. Yang, L.K. Wolf, and M.C. Messmer "Conformational Aspects of Model Chromatographic Surfaces Studied by Sum-Frequency" Anal. Chimica Acta 397, 1999, pp.81
Y. Yang, H.V. Linnerd, K.R. Williams, J.M. Riveros and J.R. Eyler "Photodetachment of Singly-Solvated Halide Ions" J. Phys. Chem. 101, 1997, pp.2371.
D. Peiris, Y. Yang, R. Ramanathan, C. Watson and J. Eyler "Infrared Multiple Photon Dissociation of Electrosprayed Crown Ether Complexes" Int. J. of Mass Spec. and Ion Processes, 157, 1996, pp.365.
Y.R. Lee, Y.J. Yang, Y.Y. Lin and S.M. Lin "Photodissociation of CBrCl3 at193 nm by Translational Spectroscopy" J. Chem. Phys. 103, 1995, pp.6966.
Y.R. Lee, Y.J. Yang, Y.Y. Lin and S.M. Lin "Photodissociation of CBrCl3 at 248 nm by Translational Spectroscopy" Chem. Phys. Lett. 222, 1994, pp.141.
Chapters in Books or Monographs
L.K. Wolf, Y.J. Yang, R.L. Pizzolatto, and M.C. Messmer “Microscopic Structure of Chromatographic Interfaces as Studied by Sum-Frequency Generation Spectroscopy” in “Interfacial Properties on the Submicron Scale” ACS/Oxford Press, 2000, 781, pp.293-30.